Analysis Platforms

The integration of external analysis platforms with the AD Knowledge Portal provides users in the AD community with an alternative to direct download, and further enables the interoperability and reuse of rich, multi-omic data from the AD Knowledge Portal.

Enabling integration between the AD Knowledge Portal and CAVATICA is a first step toward a greater goal to provide seamless, secure access to biomedical datasets made available through the Portal in as many analytical and compute environments as possible.

CAVATICA

CAVATICA was co-developed by Velsera (formerly SevenBridges) and the Center for Data Driven Discovery in Biomedicine. CAVATICA provides toolsets to support a diverse spectrum of researchers, from low-code to packed workflows to interactive analysis.

The integration of CAVATICA with the AD Knowledge Portal now provides users with multiple sophisticated tools to further analyze portal data, combine it with other research datasets, and make novel discoveries in the field of Alzheimer’s disease.

Disclaimer: Sage Bionetworks may integrate with, and provide links to, compute environments as an alternative to downloading files. These integrations or provisions do not signify an endorsement of that particular environment by Sage Bionetworks or funders, nor does it alter the relationship between Sage Bionetworks, existing data contributors, project sponsors or funders, or computational providers. 

Furthermore, it is the responsibility of individual users to review the terms of data use for each compute environment, as well as for the portal or repository from which the data is sourced. Users must personally ensure that all data access terms and conditions are met.

This page provides generic instructions on how to access, navigate, and leverage relevant tools in CAVATICA.

CAVATICA Workspace Features

The CAVATICA Analytical Workspace provides access to several types of resources and bioinformatics tools:

• Compute and Storage on AWS or Google Cloud.

• Interactive analysis with JupyterLab and R Studio, 

• Workflow execution with Common Workflow Language (CWL) and NextFlow (beta)

• Over 790 publicly available tools and workflows including MaxQuant, Olink, and FragPipe for proteomics as well as a large selection of transcriptomic tools. 

• Interactive Genome Browser and Variant Browser

Additional tools for data analysis can be found in the CAVATICA Public Apps Gallery.

CAVATICA users working with data from Sage Bionetworks-supported Portals should only use AWS for compute and storage to avoid data egress charges and higher costs for analysis.

Gaining Access

Log In to CAVATICA

To begin, visit the Compute Environments page and click the Access CAVATICA button.

• If you are new to CAVATICA, click Create an account and follow the prompts to register your account and then log in.

• If you already have a CAVATICA account, log in with your eRA Commons credentials or CAVATICA username and password. 

Connect Your CAVATICA account to Synapse

1. From the CAVATICA homepage, click on your username in the top right of the page, followed by Account settings.

2. In the top left corner of the page, click on Dataset Access.

   

3. Scroll down to the section with the heading Synapse Portal. Click Connect.

4. You will be redirected to sign in to Synapse. Log into Synapse and review the prompt requesting permission for CAVATICA to link with your Synapse account. Click Allow.

5. Your CAVATICA and Synapse accounts are now linked! You can verify that you are successfully linked by returning to the Dataset Access page, Synapse Portal section. Note that the connection will expire after a set time. If your connection expires, please repeat steps 1-4 to reconnect your account.

   

Getting Started

• This guide explains how to explore data in the AD Knowledge Portal and send the results to CAVATICA for analysis.

• Visit the CAVATICA Onboarding YouTube channel for a series of video tutorials to help you get started on the platform, create projects, add data, collaborate, manage files, and explore the Public Apps Gallery. Visit the general Velsera YouTube channel for additional webinars and videos of interest.

• Technical documentation and getting started guides can be found in the CAVATICA Knowledge Center.

• Looking for some example projects? Go to the public projects page for demo projects you can access to analyze your data.

Need more help?

The team at Sage Bionetworks is not able to provide technical support for activities in CAVATICA. General help is available any time while using CAVATICA by clicking the blue “?” on the bottom right of the screen or by emailing support@velsera.com.